I've recently gone through what you're working through buyer. I ultimately decide on the MKC over the others mainly for the following reasons:
When my wife and I test drove the NX200t we loved the look of it although I imagine that ultra sharp styling will not age well. It had good room and fantastic features. The dealership is very upscale offering their own coffee bar and free manicure/pedicure for service visits. Ultimately however we weren't impressed with the NX itself, my wife didn't care for the seat comfort, i found the touchpad interface quite annoying and the stereo was subpar for a lux vehicle imo.
Going into the test drive of the X3, on paper I thought this was going to be my choice and win out over the others. Listing out the features it looked like a clear winner. We had spent a fair bit of time in the X3 and other BMWs at the recent auto show and we're surprised at the improvements in the seat comfort and stereo since the last time we looked at them 2-3 years ago, So we were eager to drive one. I test drove the 4 cylinder since it was the closer match in price to the others. BMWs in car tech is very impressive and they do have an app coming for mobile devices although the salesman said it wouldn't have any remote start included within it. There were a few things we didn't enjoy about it however. Driving the i4 in sport mode was full adrenaline all the time, let off the gas and you feel that engine torque pull back making for sometimes a bit of a jerky ride for the passenger that's not expecting it, and yet on normal driving it felt lack lustre and dead. There didn't seem like there was a happy medium. Compared to the others the X3 also had the most interior noise while driving, and that contributed to the stereo quality a little in a bad way. The X3 however ultimately lost our interest when it came to price. We built with the salesman a 2017 X3 and the price came in $10-12k higher than either Audi or Lincoln.
Our biggest choice came down between the Q5 and the MKC, with the MKC ultimately winning. I wasn't willing to wait for the Q5 refresh and the current model even though I'd say was a little more of what I prefer to drive (with the v6), is a little outdated.
All the models have some downfalls we found, but I just depends on what you value the most out of your vehicle will help you make that decision. For us the stereo is important, comfort with enough performance to satisfy when called upon, and features for the money. We found the MKC met those requirements the best even if it wasn't the best at all 3.